1. Have (y)Our Protein Explained
HOPE
Have (y)Our Protein Explained
Marlou Snelleman
2011

2. Overview When and why do you use HOPE? How to use HOPE?
How does HOPE work?

3. When and why do you use HOPE?
HOPE is useful when you are studying (point) mutations on protein level
Using HOPE can save a lot of time
Pre-select mutations that are expected to have effect
Quick information without examining multiple databases and programs
No need for complete knowledge of bioinformatics

4. How to use HOPE?
HOPE needs the sequence as input

5. How to use HOPE?

6. Structural information Comparison of properties
How does HOPE work?
Input
BLAST
PDB
Structure or model
Structural analysis
Structural information
Output
No structure
DAS-servers
Additional information
Uniprot
HSSP
Conservation scores
Comparison of properties

7. Input BLAST The sequence Object: The sequence The mutation Tool: BLAST
Information:
Uniprot
Additional information
Domains, active sites, phosphorylation sites, contacts, cysteine bridges, variants etc.
PDB
Structural information

8. Uniprot Database that contains Protein sequences Protein information
Function
Origin
Position of active site(s)
Position of phosphorylation site(s)
Domains
Etc.
Cross-links to other databases

9. PDB Structure or model 100% identity? Less than 100% identity?
Use this PDB structure
Less than 100% identity?
Make a model
when the sequences are longer than 80 amino acids and the identity is higher than 25% (Sander and Schneider curve)
with the YASARA and WHAT IF Twinset

10. Structure or model Structural analysis
Object: Structure or model
Tool: WHAT IF
Information: Clashes, disturbed contacts, etc.

11. PDB No structure Object: The sequence Tool: DAS-servers
Information: prediction of for example phosphorylation sites.

12. HSSP Conservation scores
Object: The sequence
Tool: HSSP
Information: conservation scores
Comparison of properties
Object: The wild type and the mutant amino acids
Information: comparison of the different properties of the amino acids

13. Output
Print screen van een report

14. One example: LRTOMT Mutations in the LRTOMT gene cause deafness
One of these mutations: Y111L

15. One example: LRTOMT
HOPE: